Detecting repeated 3D protein substructures has become a new crucial frontier in motifs inference. In [7] we have suggested a possible solution to this problem by means of a new framework in which the repeated pat- tern is required to be conserved also in terms of relations between its position pairs. In our application these relations are the distances be- tween α-carbons of amino acids in 3D proteins structures, thus leading to a structural consensus as well. In this paper we motivate some com- plexity issues claimed (and assumed, but not proved) in [7] concerning inclusion tests between occurrences of repeated motifs. These inclusion tests are performed during the motifs inference in KMRoverlapR (pre- sented in [7]), but also within other motifs inference tools such as KMRC ([9]). These involve alternative representations of motifs, for which we also prove here some interesting properties concerning pattern matching issues. We conclude this contribution with a few tests on cytochrome P450 protein structures.

Implicit and Explicit Representation of Approximated Motifs

PISANTI, NADIA;
2006-01-01

Abstract

Detecting repeated 3D protein substructures has become a new crucial frontier in motifs inference. In [7] we have suggested a possible solution to this problem by means of a new framework in which the repeated pat- tern is required to be conserved also in terms of relations between its position pairs. In our application these relations are the distances be- tween α-carbons of amino acids in 3D proteins structures, thus leading to a structural consensus as well. In this paper we motivate some com- plexity issues claimed (and assumed, but not proved) in [7] concerning inclusion tests between occurrences of repeated motifs. These inclusion tests are performed during the motifs inference in KMRoverlapR (pre- sented in [7]), but also within other motifs inference tools such as KMRC ([9]). These involve alternative representations of motifs, for which we also prove here some interesting properties concerning pattern matching issues. We conclude this contribution with a few tests on cytochrome P450 protein structures.
2006
Pisanti, Nadia; Soldano, H; Carpentier, M; Pothier, J.
File in questo prodotto:
Non ci sono file associati a questo prodotto.

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11568/104725
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus ND
  • ???jsp.display-item.citation.isi??? ND
social impact